New update (v1.7.5): Using saved color mappings supported in command line mode (see -? for details, check the -cm switch). You'll have to use the GUI to create the color mappings.
I also fixed a bug in the GUI version: the mapping selected at startup was the last saved mapping, not the last used.

(after some pondering over resulting documents produced by Scribble Merger): Is it possible to implement merging scribbles into PDF document so we could delete/update them later. Currently, after scribbles been merged with PDF document, they becomes irreversibly embedded into PDF document as the images(?).

What I would like to see - instead of converting Iliad scribbles into images, having them embedded as a "line objects/lines" (not sure if I'm using the right term here). Having scribbles as "lines" allow us to remove or update them on PC as well.

I believe the "line" (*1)(*2) is the 2nd most popular tool (the number one is the highlighting but highlights doesn't really work nice on the 16-grayscale Iliad's screen) to make notes "on" PDF documents.

Moreover, we would be able to convert these "line" objects back to Iliad's scribbles - so we could even delete/update them on Iliad! This would really make note taking a two-way process.